A security vulnerability called BEAST (Browser Exploit Against SSL/ TLS ) is currently in the news. This leverages weaknesses in cipher block chaining to exploit the SSL protocol. This has the potential to affect any SSL encrypted communications and thus requests to communicate with Serena Deployment Automation (SDA) are affected.
This problem is caused by a configuration change in the new Java plug-in that attempts to protect against a Man-In-The-Middle attach, which all previous JRE versions were prone to when using TLS encryption (which includes SSL v3). Details on the problem can be found here: http://java.sun.com/javase/javaseforbusiness/docs/TLSReadme.html